Binding Profiles Based on Normal Mode Analysis as a Foundation for a Unified Approach to Allosteric Activation of Prolactin Receptor

Abstract

Two of the most fundamental biological processes are ligand binding and allosteric signaling. Despite their (often) direct linkage, a unified model of the underlying dynamics is not well established. The harmonic motions identified by normal mode analysis (NMA) provide a natural coordinate system for conformation space. Binding profiles and allosteric profiles based on NMA allow for a unified model which describes the propensity for various structure motions to promote/inhibit binding and allosteric activation. The authors have recently developed the allosteric model; the current work presents the binding model.The normal modes describe local motions accessible to a conformation. Each of the modes is followed over a small displacement, leading to a set of new conformations. This procedure is repeated to generate an ensemble, where each conformation is defined by its sequence of normal modes. Ensembles are generated around a receptor and ligand. Each receptor conformation is paired against each ligand conformation and scored for: (1) compatibility of interface shape; and (2) compatibility of interface dynamics. These scores are attributed to the normal mode sequences associated with each candidate conformation. The scores are summed over all possible conformation pairings, producing a binding profile that defines each normal mode's propensity to contribute to compatible interface shape and interface dynamics.The prolactin receptor dimerizes and preferentially binds prolactin at one binding site, and then binds another prolactin at the second binding site - activating the receptor. Binding profiles are generated for prolactin and prolactin receptor, isolated from the various complexes along the activation pathway. The goal is to identify the dynamics that regulate binding site preference and allosteric activation. Future work will incorporate NMR studies to validate and refine the initial results.